lgcpST: Alternative to lgcpPredictSpatioTemporalPlusPars

In realTimeSurv: Real Time Disease Surveillance Using Geospatial Statistical Modelling

Description

Internal function and alternative to lgcp::lgcpPredictSpatioTemporalPlusPars.

Usage

lgcpST(
  formula,
  xyt,
  T,
  laglength,
  ZmatList = NULL,
  model.priors,
  model.inits = lgcpInits(),
  spatial.covmodel,
  cellwidth = NULL,
  poisson.offset = NULL,
  mcmc.control,
  output.control = setoutput(),
  gradtrunc = Inf,
  ext = 2,
  inclusion = "touching"
)

Arguments

formula	a formula object of the form X ~ var1 + var2 etc. The name of the dependent variable must be "X". Only accepts 'simple' formulae, such as the example given.
xyt	An object of class stppp
T	the time point of interest
laglength	the number of previous time points to include in the analysis
ZmatList	A list of design matrices Z constructed with getZmat and possibly addTemporalCovariates see the details below and Bayesian_lgcp vignette for details on how to construct this.
model.priors	model priors, set using lgcpPrior
model.inits	model initial values. The default is NULL, in which case lgcp will use the prior mean to initialise eta and beta will be initialised from an oversispersed glm fit to the data. Otherwise use lgcpInits to specify.
spatial.covmodel	choice of spatial covariance function. See ?CovFunction
cellwidth	the width of computational cells
poisson.offset	A list of SpatialAtRisk objects (of length the number of types) defining lambda_k (see below)
mcmc.control	MCMC paramters, see ?mcmcpars
output.control	output choice, see ?setoutput
gradtrunc	truncation for gradient vector equal to H parameter Moller et al 1998 pp 473. Default is Inf, which means no gradient truncation, which seems to work in most settings.
ext	integer multiple by which grid should be extended, default is 2. Generally this will not need to be altered, but if the spatial correlation decays slowly, increasing 'ext' may be necessary.
inclusion	criterion for cells being included into observation window. Either 'touching' or 'centroid'. The former, the default, includes all cells that touch the observation window, the latter includes all cells whose centroids are inside the observation window.

Details

A copy of lgcp::lgcpPredictSpatioTemporalPlusPars that parallelises the sampler and produces a reduced output and lgcpReal object. See help(lgcpPredictSpatioTemporalPlusPars) for more information.

Value

an object of class lgcpPredictSpatioTemporalPlusParameters

realTimeSurv documentation built on May 18, 2021, 9:07 a.m.